Fig. 2

Analysis of differentially expressed genes in TSCs and TGCs. a Venn diagrams showing the number of differentially expressed upregulated (left) and downregulated (right) genes in TSCs and TGCs identified through DESEQ2 (dark gray), EdgeR (light gray), and both (overlap) programs. b Integrated genome viewer (IGV) snapshot of the Fgfr2 locus illustrating read coverage in all 3 replicates of TSCs and TGCs. Reference gene track is shown at the bottom (gray line) with bars representing the corresponding exons and arrowhead (black) showing gene orientation. c IGV snapshot displaying the read coverage within the Pl-1 gene, a known marker of TGCs, in all 3 replicates of undifferentiated and differentiated cells.d mRNA expression analysis of 8 selected upregulated genes using real-time PCR. Expression of Pl-1 was used as a marker for TGCs. e mRNA expression analysis of 8 selected downregulated genes identified through real-time PCR. Amplification of Fgfr2 was used as a known marker of TSCs. Error bars represent SEM of 3 independent biological replicates. f Classification of differentially expressed genes to functionally distinct classes of protein families. g PANTHER pathway enrichment of differentially expressed genes in TGCs.